Technical Abstract:
Genomic regions associated with general disease (respiratory disease, foot rot, and pinkeye) in beef cattle were identified using treatment records on 2,849 animals. General disease cases included animals treated for bovine respiratory disease, foot rot, or pinkeye. Untreated cohorts, matched on breed composition and contemporary group, for cases were included as controls. Fifteen pools of DNA with 102 cases/pool and 13 pools with an average of 101 controls/pool were genotyped using 777,000 single nucleotide polymorphisms (SNP). Mixed model methods were used to estimate differences in allele frequency between cases and controls while accounting for technical variation (specific to SNP array platform), binomial sampling and pool construction error. Hidden population structure unaccounted by the matching procedure was considered statistically using eigenvectors of the correlation among pools across all SNP. Single nucleotide polymorphisms residing on chromosomes 3, 6, 7, 20, 23, and X were highly significant (nominal P < 0.00001). Three of these SNPs reside on chromosome 3 between 25 megabase (Mb) and 26 Mb. Fourteen additional SNPs were also significant (P < 0.001) in this chromosomal region. On chromosome 6, one highly significant SNP (P < 0.00001) is located between 63 and 64 Mb. In this genomic region, ten additional SNPs were also significant (P < 0.001). Two SNPs were highly significant (P < 0.00001) on chromosome 7. One resides on Mb 56, while the other resides on the telomeric end of the chromosome. One SNP was highly significant (P < 0.00001) on chromosome 20 (on 55 Mb), and one on chromosome 23 (on 20 Mb). Three SNPs on chromosome X were highly significant (P < 0.00001). These SNPs reside at 12, 21, and 94 Mb. Results from this study, combined with future studies in a meta-analysis, should provide strong evidence for these genomic regions as harboring genes associated with defense mechanisms against pathogens.